[Genome] gene structure table

[Ann Zweig]

Hello Dorit,

	If I understand your question correctly, then, yes there should be a way to do 
this using our web tools.  I just need a little more information from you 
regarding exactly what you are trying to do, then I can give you detailed 
instructions.

- Are you working on the latest human assembly (hg18, Mar. 2006)?

- Do you have a list of the mRNAs that you are interested in, or do you need to 
generate those with our tables as well?

- What type of GeneIDs do you have: e.g. SwissProt, RefSeq, UCSC Known Gene, etc.

	After you answer those questions, I should be able to help you better.

	Until then, you might take a look at our Table Browser (press the "Tables" link 
in the blue navigation bar).  The Known Gene table contains protein coding genes 
based on proteins from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their 
corresponding mRNAs from GenBank.  It is linked to many other tables including 
the kgXref table that contains links between a Known Gene ID and other aliases.

	In the table browser, you can also access the table which underlies the mRNA 
track (table is called: all_mrna).

	This may be enough to get you started.  But please do feel free to reply back 
to me with the answers to those questions and a little more detail about exactly 
what you want, and I will try to give you more detailed instructions.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Dorit Shweiki wrote:
> Dear Colleague,
>  
> We are looking for a way to extract a table describing human gene
> structure, in order to see whether mRNAs (not refseq records) which have
> no polyA tail are ending at the terminal exon or internal one. The only
> table we found with exons coordinates relates to mRNA accession and not
> to GeneID.
>  
> Is there a way to extract such a table which is sorted by geneID (and
> includes all known variants for this gene)?
>  
> Thank you in advance
> Dorit Shweiki
>  
> **********************************************************************
> Dorit Shweiki, Ph.D.,
> Head, Bioinformatics Program
> Computer Science Department
> The Academic College of Tel Aviv Yaffo
> dorits at mta.ac.il
> Tel: 972-3-5211853
> Fax: 972-3-5211871
> **********************************************************************
>  
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